The present paper contains the results of our microbiological and biogeochemical investigations carried out during a series of expeditions to the White Sea in 2002–2006. The studies were conducted in the open part of the White Sea, as well as in the Onega, Dvina, and Kandalaksha bays. In August 2006, the photosynthetic productivity in the surface water layer was low (47–145 mg C m−2 day−1). Quantitative characteristics of microbial numbers and activity of the the key microbial processes occurring in the water column of the White Sea were explored. Over the 5-year period of observations, the total number of bacterial cells in the surface layer of the water column varied from 50 to 600 thousand cells ml−1. In August 2006, bacterioplankton production (BP) was estimated to be 0.26–3.3 μg C l−1 day−1; the P/B coefficient varied from 0.22 to 0.93. The suspended organic matter had a lighter isotope composition (from −28.0 to −30.5‰) due to the predominance of terrigenous organic matter delivered by the Northern Dvina waters. The interseasonal and interannual variation coefficients for phytoplankton production and BP numbers are compared. The bacterioplankton community of the White Sea's deep water was found to be more stable than that of the surface layer. In the surface layer of bottom sediments, methane concentration was 0.2–5.2 μl dm−3; the rate of bacterial sulfate reduction was 18–260 μg S dm−3 day−1; and the rates of methane production and oxidation were 24–123 and 6–13 nl CH4 dm−3 day−1, respectively. We demonstrated that the rates of microbial processes of the carbon and sulfur cycles occurring in the sediments of the White Sea basin were low.